Place squash, onion and butter in a big enough saucepan and saute until tender; but still crisp. Fold in chilies, flour, salt and pepper.
Place in a greased 2-quart baking dish; sprinkle with Monterey cheese.
Combine egg, cottage cheese, parsley and chives. Layer over Monterey cheese, sprinkle with Parmesan.
Bake uncovered at 400 degrees for 25-30 minutes until heated through.
(I Have Used a Combination of Pepper Jack, cheddar and monterey, with great results)